X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 20% PEG 3350, 200 mM Ca Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.26 α = 90
b = 88.26 β = 90
c = 134.4 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.66 50 100.0 0.082 -- -- 11.0 23956 23956 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.66 1.69 100.0 0.654 -- -- 9.3 1183

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.662 26.541 -- 1.34 23952 23952 1999 99.94 0.1636 0.1636 0.1617 0.1842 random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.6619 1.7035 -- 140 1537 0.2623 0.2934 -- 100.0
X Ray Diffraction 1.7035 1.7495 -- 141 1547 0.2088 0.2116 -- 100.0
X Ray Diffraction 1.7495 1.801 -- 142 1560 0.1786 0.2029 -- 100.0
X Ray Diffraction 1.801 1.8591 -- 139 1528 0.1579 0.1818 -- 100.0
X Ray Diffraction 1.8591 1.9255 -- 143 1561 0.1411 0.1636 -- 100.0
X Ray Diffraction 1.9255 2.0026 -- 142 1557 0.1423 0.1943 -- 100.0
X Ray Diffraction 2.0026 2.0937 -- 142 1561 0.1456 0.173 -- 100.0
X Ray Diffraction 2.0937 2.204 -- 142 1562 0.1546 0.186 -- 100.0
X Ray Diffraction 2.204 2.3421 -- 143 1569 0.1551 0.191 -- 100.0
X Ray Diffraction 2.3421 2.5228 -- 143 1570 0.1545 0.1798 -- 100.0
X Ray Diffraction 2.5228 2.7764 -- 142 1566 0.1602 0.1771 -- 100.0
X Ray Diffraction 2.7764 3.1776 -- 143 1579 0.163 0.1942 -- 100.0
X Ray Diffraction 3.1776 4.0012 -- 146 1596 0.1478 0.1611 -- 100.0
X Ray Diffraction 4.0012 26.5448 -- 151 1660 0.1746 0.1878 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.1456
Anisotropic B[1][1] 0.7221
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.7221
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.4442
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.012
f_bond_d 0.007
f_angle_d 1.152
f_chiral_restr 0.072
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1309
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 162

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL-2000 data reduction
PHENIX phasing